Freestyle External Contour has Large Gaps. Error Related to Topology?
I ran into a similar issue, in my opinion this is a bug ocurring when working with larger geometries. Try scaling your geometry down (dimensions below 100 units) and try again.

For bigger geometries sometimes whole lines or part of lines (always when crossing with hidden lines as seen from the camera) are disappearing, this goes away when simply scaling down. See the screenshots below.







I've file a bug report here, including a testfile: https://developer.blender.org/T49479

Update: According to the bug report, this bug has been fixed end of December 2016 and should not occur anymore in newer versions of blender.